[R] anova

Bert Gunter gunter.berton at gene.com
Thu Aug 21 16:37:38 CEST 2014

```... and you do get P values; you just don't understand what you're
looking at, which is more or less what you said.

This is not a statistical help site. You should seek local statistical
consulting advice or post on a statistical help site (caveat emptor!)
like stats.stackexchange.com, not here.

Cheers,
Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll

On Thu, Aug 21, 2014 at 3:13 AM, Lynn Govaert <lynn.govaert at gmail.com> wrote:
> I pressed enter to soon.
>
> Again
>
> Hi all,
>
> I have troubles with doing an anova. So I have the following variables: a
> variable group with two levels, a continuous variable trait and within each
> group we have 12 organisms (clone) and for each clone we have 5 replicates.
> So we want to see if for the variable trait the two groups differ,
> including the information for the clones.
>
> So the dataset looks like:
>
> trait          group            clone
> ...              1                   a1
> ...              1                   a2
> ...
> ...              1                   a12
> ...              1                    a1
> ...
> ...               2                    b1
> ...               2                    b2
>
> etc
>
> trait are just some numbers.
> So clone is nested in group.
>
> Then I don't understand how to make the anova,
> I was thinking we want to see if there is an effect of group
>
> So we built the model aov(trait ~group)
> but because we also want to include the effect of clone which is a random
> effect we do
>
> aov(trait ~ group + Error(clone))
> but because Clone is nested in group
> we do
> aov(trait ~ group + Error(group/clone))
>
> but if I do this I get the following output
>
>
> Error: PopulationTNFMF
>                 Df  Sum Sq Mean Sq
> PopulationTNFMF  1 0.00917 0.00917
>
> Error: PopulationTNFMF:CloneTNFMF
>           Df    Sum Sq   Mean Sq F value Pr(>F)
> Residuals  1 0.0001849 0.0001849
>
> Error: Within
>            Df  Sum Sq   Mean Sq F value Pr(>F)
> Residuals 117 0.02107 0.0001801
>
>
> and I don't get any p-values, so I guess I'm doing something wrong.
> Can someone help?
>
> Lynn
>
>
> 2014-08-21 12:08 GMT+02:00 Lynn Govaert <lynn.govaert at gmail.com>:
>
>> Hi all,
>>
>> I have troubles with doing an anova. So I have the following variables: a
>> variable group with two levels, a continuous variable trait and within each
>> group we have 12 organisms (clone) and for each clone we have 5 replicates.
>> So we want to see if for the variable trait the two groups differ,
>> including the information for the clones.
>>
>> So the dataset looks like:
>>
>> trait          group
>>
>
>         [[alternative HTML version deleted]]
>
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